Identification of G1-regulated genes in normally cycling human cells. by Maroun J Beyrouthy, Karen E Alexander, Amy Baldwin, Michael L Whitfield, Hank W Bass, Dan McGee, Myra M Hurt

“…<h4>Methodology and findings</h4>We used a robotic mitotic shake-off apparatus to select cells in late mitosis for genome-wide gene expression studies. …”
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Clustering, Pathway Enrichment, and Protein-Protein Interaction Analysis of Gene Expression in Neurodevelopmental Disorders by Ruchi Yadav, Prachi Srivastava

“…In this study, we have used four samples of microarray neuronal developmental data: control, RV (resveratrol), NGF (nerve growth factor), and RV + NGF. …”
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Integrating single-cell RNA sequencing, WGCNA, and machine learning to identify key biomarkers in hepatocellular carcinoma by Gang Wang, Jiaxing Zhang, Yirong Li, Yuyu Zhang, Weiwei Dong, Hengquan Wu, Jinglan Wang, Peiqing Liao, Ziqiang Yuan, Tao Liu, Wenting He

“…Abstract The microarray and single-cell RNA-sequencing (scRNA-seq) datasets of hepatocellular carcinoma (HCC) were downloaded from the Gene Expression Omnibus (GEO) database. …”
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Identification of potential biomarkers for 2022 Mpox virus infection: a transcriptomic network analysis and machine learning approach by Joy Prokash Debnath, Kabir Hossen, Sabrina Bintay Sayed, Md. Sayeam Khandaker, Preonath Chondrow Dev, Saifuddin Sarker, Tanvir Hossain

“…This study aimed to identify the differentially expressed genes (DEGs) induced by the 2022 MPXV infection through comprehensive bioinformatics analyses of microarray and RNA-Seq datasets from post-infected cell types with different MPXV clades. …”
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Decrease in pneumococcal co-colonization following vaccination with the seven-valent pneumococcal conjugate vaccine. by Carina Valente, Jason Hinds, Francisco Pinto, Silvio D Brugger, Katherine Gould, Kathrin Mühlemann, Hermínia de Lencastre, Raquel Sá-Leão

“…Co-colonization, serotype identification, and relative serotype abundance were detected by analysis of DNA of the total bacterial growth of the primary culture plate using the plyNCR-RFLP method and a molecular serotyping microarray-based strategy. …”
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Expression of Genes Related to Germ Cell Lineage and Pluripotency in Single Cells and Colonies of Human Adult Germ Stem Cells by Sabine Conrad, Hossein Azizi, Maryam Hatami, Mikael Kubista, Michael Bonin, Jörg Hennenlotter, Karl-Dietrich Sievert, Thomas Skutella

“…Genome-wide comparisons with microarray analysis confirmed that different haGSC colonies exhibited gene expression heterogeneity with more or less pluripotency. …”
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The significance of long chain non-coding RNA signature genes in the diagnosis and management of sepsis patients, and the development of a prediction model by Yong Bai, Jing Gao, Yuwen Yan, Xu Zhao

“…The purpose of this study was to determine the value of Long chain non-coding RNA (LncRNA) RP3_508I15.21, RP11_295G20.2, and LDLRAD4_AS1 in the diagnosis of adult sepsis patients and to develop a Nomogram prediction model.MethodsWe screened adult sepsis microarray datasets GSE57065 and GSE95233 from the GEO database and performed differentially expressed genes (DEGs), weighted gene co-expression network analysis (WGCNA), and machine learning methods to find the genes by random forest (Random Forest), least absolute shrinkage and selection operator (LASSO), and support vector machine (SVM), respectively, with GSE95233 as the training set and GSE57065 as the validation set. …”
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Transcriptional Profile of Kidney from Type 2 Diabetic db/db Mice by Haojun Zhang, Tingting Zhao, Zhiguo Li, Meihua Yan, Hailing Zhao, Bin Zhu, Ping Li

“…The top 10 hub genes were selected from the constructed PPI network of DEGs, including Ccnb2 and Nr1i2, which remained largely unclear in DN. …”
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Identification of Differentially Expressed Genes and Long Noncoding RNAs Associated with Parkinson’s Disease by Lu-Mei Chi, Li-Ping Wang, Dan Jiao

“…This study aims to determine differentially expressed genes (DEGs) and long noncoding RNAs (lncRNAs) associated with Parkinson’s disease (PD) using a microarray. Methods. We downloaded the microarray data GSE6613 from the Gene Expression Omnibus, which included 105 samples. …”
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Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72. by Abhijit Sarkar, Barbara Reinhold-Hurek

“…For selected genes, differential expression was corroborated by real time RT-PCR studies.…”
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Gene expression profiles in Parkinson disease prefrontal cortex implicate FOXO1 and genes under its transcriptional regulation. by Alexandra Dumitriu, Jeanne C Latourelle, Tiffany C Hadzi, Nathan Pankratz, Dan Garza, John P Miller, Jeffery M Vance, Tatiana Foroud, Thomas G Beach, Richard H Myers

“…Single-nucleotide polymorphisms (SNPs) selected from a recent meta-analysis of PD genome-wide association studies (GWAS) were successfully genotyped in 50 out of the 53 microarray brains, allowing a targeted expression-SNP (eSNP) analysis for 52 SNPs associated with PD affection at genome-wide significance and the 189 probes from FoxO1 regulated genes. …”
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Molecular profiles of tumor contrast enhancement: A radiogenomic analysis in anaplastic gliomas by Xing Liu, Yiming Li, Zhiyan Sun, Shaowu Li, Kai Wang, Xing Fan, Yuqing Liu, Lei Wang, Yinyan Wang, Tao Jiang

“…Gene set enrichment analysis (GSEA), significant analysis of microarray, generalized linear models, and Least absolute shrinkage and selection operator algorithm were used to explore radiogenomic and prognostic signatures of AG patients. …”
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Identifying a unique chromosomal pattern to predict the gemcitabine response in patients with cholangiocarcinoma by Sutheemon Techa-ay, Sasithorn Watcharadetwittaya, Raksawan Deenonpoe, Prakasit Sa-ngiamwibool, Chanita Panwoon, Watcharin Loilome, Poramate Klanrit, Anchalee Techasen, Yaovalux Chamgramol, Manida Suksawat, Napat Armartmuntree, Thomas O’Connor, Hideyuki Saya, Malinee Thanee

“…To predict the response to GEM, we evaluated chromosomal aberrations using a chromosome microarray, and their association with GEM response by histoculture drug response assay. …”
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A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome. by Katherine James, Shereen Al-Ali, Jessica Tarn, Simon J Cockell, Colin S Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin T Pease, Paul Emery, Peter Lanyon, John A Hunter, Monica Gupta, Michele Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, UK Primary Sjögren’s Syndrome registry, Anil Wipat, Julia Newton, David E Jones, John Isaacs, Jennifer Hallinan, Wan-Fai Ng

“…Finally, gene set enrichment analysis (GSEA) was used as a feature selection technique for input into a support vector machine (SVM) classifier. …”
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Identification of Hub Biomarkers and Immune and Inflammation Pathways Contributing to Kawasaki Disease Progression with RT-qPCR Verification by Hongjun Ba, Lili Zhang, Huimin Peng, Xiufang He, Yuese Lin, Xuandi Li, Shujuan Li, Ling Zhu, Youzhen Qin, Xing Zhang, Yao Wang

“…Patients and Methods. Gene microarray data were collected from the Gene Expression Omnibus database. …”
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Global gene expression profiling reveals SPINK1 as a potential hepatocellular carcinoma marker. by Aileen Marshall, Margus Lukk, Claudia Kutter, Susan Davies, Graeme Alexander, Duncan T Odom

“…Six genes identified by microarray as highly expressed in HH-HCC were confirmed by RT qPCR. …”
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Epidemiology of group B streptococcal infection in pregnant women and diseased infants in mainland China by Jing Huang, Xin-Zhu Lin, Yao Zhu, Chao Chen

“…Serotype III was the dominant serotype that was observed in GBS isolates. GBS detection and identification has become more commonplace, due to the availability of polymerase chain reaction and DNA microarray technologies. …”
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Signature-based small molecule screening identifies cytosine arabinoside as an EWS/FLI modulator in Ewing sarcoma. by Kimberly Stegmaier, Jenny S Wong, Kenneth N Ross, Kwan T Chow, David Peck, Renee D Wright, Stephen L Lessnick, Andrew L Kung, Todd R Golub

“…<h4>Methods and findings</h4>A gene expression signature for the EWS/FLI off state was determined with microarray expression profiling of Ewing sarcoma cell lines with EWS/FLI-directed RNA interference. …”
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Increased cycling cell numbers and stem cell associated proteins as potential biomarkers for high grade human papillomavirus+ve pre-neoplastic cervical disease. by Maurice Canham, Chara Charsou, June Stewart, Sharon Moncur, Laura Hoodless, Ramya Bhatia, Duanduan Cong, Heather Cubie, Camille Busby-Earle, Alistair Williams, Victoria McLoughlin, John D M Campbell, Kate Cuschieri, Sarah Howie

“…As cancer is increasingly presumed to develop from proliferative, tumour initiating, cancer stem cells (CSCs), and as other oncogenic viruses induce stem cell associated gene expression, we evaluated whether presence of mRNA (detected by qRT-PCR) or proteins (detected by flow cytometry and antibody based proteomic microarray) from stem cell associated genes and/or increased cell proliferation (detected by flow cytometry) could be detected in well-characterised, routinely collected cervical samples from high risk HPV+ve women. …”
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Immune Condition of Colorectal Cancer Patients Featured by Serum Chemokines and Gene Expressions of CD4+ Cells in Blood by Takuya Komura, Masaaki Yano, Akimitsu Miyake, Hisashi Takabatake, Masaki Miyazawa, Norihiko Ogawa, Akihiro Seki, Masao Honda, Takashi Wada, Shigeyuki Matsui, Shuichi Kaneko, Yoshio Sakai

“…The differences in gene expression profiles of whole blood cells and cell subpopulations between CRC patients and healthy controls were analyzed using DNA microarray. Serum cytokine/chemokine concentrations in CRC patients and healthy controls were measured via multiplex detection immunoassays. …”
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